Neon Genesis Evangelion: The Fourth Apocalypse
by kayarn
Summary: Third Impact has been halted by the actions of one boy and the world has returned to what passes for normalcy. However SEELE has not been defeated and are planning a new attempt to achieve instrumantality. Can Shinji save humanity once again?
1. The Worlds Rebirth

Neon Genesis Evangelion: The Fourth Apocalypse 

Disclaimer: I don't own Evangelion, its characters, technology or anything else related to the show, so please don't sue me 'cause I don't have anything worth taking.

Note: This is my first fanfiction so please don't judge me too harshly for it. I'll try to keep the characters in character but there will be some occurrences of OOC' ness so please forgive me for it. It takes place just after the events in the end of Evangelion. Characters thoughts are in brackets i.e. ( ).

Chapter 1: The world's Rebirth.

The black haired boy lay on the beach in the same position he occupied for the last two hours as the red waves continued to break against the beaches white sand. The world had become a desolate reflection of its former glory. The dismembered head of the new 'god' continued to settle into the sea. "What did I stop it for? ", the boy finally spoke to no one in particular. " I 'saved the world'. What a joke. I've hurt more people in saving the world than the angels ever did. Even Rei, Misato and … Auska…". The boy choked back a sob as his voice finally broke and he stole a glance at the injured redhead lying at his side. She had not moved or spoken since he had tried to kill her for the second time. Shinji continued to cry as the waves continued to break.

After what seemed like hours of crying Shinji finally looked up. Across the waves he could still see the head of the final Rei, the white of the head contrasting sharply with the red of the sea. "Ayanami I'm so sorry. If I could bring the world back I would but…". Suddenly a soft voice interrupted him, "Why do you refuse to do something that is in your power pilot Ikari? ". Rei appeared in front of Shinji in the now familiar school uniform and looked down at Shinji, "You who have stopped Third Impact have the power to restore the world as it was or remake the world as you see fit. It is in your power to restore the lives of everyone who was lost as a result of your fathers naked ambition and selfishness." Shinji slowly looked up at her and stared at her red eyes. "Ayanami, I…I just don't know.  The world caused so much pain and suffering. How can I bring back the world when I know what I'll be bringing back? The greed, hate and pain. HOW CAN I DO IT!". 

With this final scream Auska finally awoke. "BAKA… what's all the noise about? Are you still obsessing over your choice? Well stop it. The choice was made Shinji so now you have to deal with it. From what I caught while I was semi conscious was that you don't want to bring back the evils of the world, well that's a load of bull. Haven't you learned anything by now, you can't have the good without the bad. Just remember you'll be bringing back the good people too, people like Misato, Hikari, Maya and even your baka friends! You just have to remember that everything exists in balance, you just have to find the right balance." Auska placed her uninjured arm on Shinji's right shoulder, "I trust you to make the right decision Shinji, I saw your mind Shinji and I know you're the person most deserving of this choice." Rei slowly moved to Shinji's other side and placed her hand on his other shoulder, "Both of us trust you Shinji and we know you will make the right choice. I believe in you my brother. I trust you."

"Thank you. With you supporting me I know I can make the right choice. Just promise me one thing, promise me you will stay with me. Both of you." When both girls signaled their agreement Shinji smiled, one of his rare happy smiles. "Lets do this. I'll try to do what's right, for everyone." Shinji slowly closed his eyes and concentrated hard on the world he wanted to restore, on all the people he wanted to see again, his friends he wanted to see again, his sister and the red headed girl who occupied his heart. Slowly a kaleidoscope of light and color began to spread around the shattered world as Shinji attempted to reform the world that was destroyed by SEELE… and his Father. As the majestic light show faded the three teens found themselves standing on the lookout above the ruined city of Tokyo-3. Shinji looked around and marveled at the world that he had restored, the people he had saved and the future he had assured for the rest of humanity. "Rei, Auska, lets go home."

X

In the underground command center of Nerv sub Commander Fuyutski slowly pulled himself to his feet. The last thing he remembered was seeing Yui and dissolving into LCL. Yet here he was solid and with no Yui in sight, "What the hell is going on? Give me a status report Hyuga." The spectacled man dragged himself to his console and punched in a few commands. "Commander external sensors are back online but there is no trace of the anti AT field, the JSSDF forces or any operational Eva's out there. Unit 1 is currently lying at the bottom of the Tokyo-3 Lake. The remains of unit 2 are lying where they were before. The links to the pilots are down so we can't even tell if the pilots are in their Eva's let alone if they are alive or dead. The SEELE Eva's are all deactivated with no emissions coming from them; their S2 organs appear to be offline. All traces of damage from the SSDF attack are gone, no crater from the N2 mine and no internal damage from the commando attack. In fact there are no casualties, no injuries and no fatalities. All our personnel are either unconscious or just awake. The JSSDF have vanished and everything is relatively normal."

"How can this be possible? Third Impact occurred, we should all be dead.", the commander replied. Suddenly an image of Shinji crossed his mind and he knew what happened. "Thank you Shinji, we owe you another one. Aoba try to locate the pilots and get me a fix on commander Ikari and doctor Akagi. Ibuki get recovery teams out there to salvage all the eva's, that includes the SEELE eva's and the remains of unit 2. Get to work." The longhaired man and the young woman snapped to their tasks as the commander continues to give orders. "Hyuga find major Katsuragi and update her on the situation. Get the magi working on what happened out there and get me an explanation on why we are still here, I also want ides on how to adapt the SEELE Eva technology to use on our own units. I also want to know if it is possible to regenerate unit 2. Well get to it!" . The bridge bunnies swung into action to follow his orders and the bridge became a riot of activity. Orders were shouted people ran across the bridge with orders, technicians checked the magi system for damage and people just trying to get a handle on the situation. On his own raised seat above the chaos Fuyutski smiled to himself, " (You greatly underestimated your own son Gendo. You believed he did not have the strength or the will to oppose your plans but he alone stopped the apocalypse and if you are still alive you will have a lot to answer for, not just to him but also to the whole world.  But I know it's not over. SEELE will return and Shinji will once again have to be mankind's champion to defend us from another impact. You have placed so much responsibility on that young mans shoulders. I will help him to realize his potential. Gendo you are no longer needed in this world and that fact gives me a profound sense of relief.)"

X

Deep in the bowels of Nerv Misato Katsuragi slowly awakened. Surprisingly she felt pretty good for someone who had been shot. She no longer felt any pain; there weren't any bullet holes, only a small pool of blood on the floor. "What the hell happened to me? How can I still be alive after the shot I took?". The same image of Shinji came to her just like the commander. "Thank you Shinji you saved us after all." Pulling out her cell phone she hit the third button on her speed dial that was picked up almost immediately. " Hyuga give me a status report." "Good to hear from you Major. So far we have determined that something interrupted third impact. We have down eva's all over the landscape, no info on our pilots. All the SEELE eva's are down too. All JSSDF forces have mysteriously vanished, all damage has been mysteriously repaired and we're tying to ascertain what happened. Commander Fuyutski wants you to get up to the bridge right away." "Alright I'm on my way. I should be there in a few minutes." Misato casually thumbed the disconnect button on her cell. "Shinji we owe you another big one and somehow I don't think a deluxe dinner on me is gonna cover it this time. Well time to get moving." 

X

Through the ruined streets of Tokyo-3 the pilots walked, trying to find their way home. As usual Rei was encapsulated in her own world, Shinji was reflecting quietly on what happened and Auska seemed to complain more loudly the more they walked. "How much longer Shinji, my feet hurt and in case you haven't noticed I'M INJUIRED!" Shinji let out another exasperated sigh and replied, "Just another few minutes Auska and we'll be home and you can have a good long rest." Rei as usual didn't reply but kept walking. All three had been traveling for hours and the fatigue was starting to show on all of them. Although Auska was too stubborn to admit it she was ready to drop with exhaustion and hat to be supported by Shinji. Rei was just as tired but wasn't as vocal as Auska was. She decided to suffer in silence. Shinji was aware of the girl's problems but could do nothing to ease their pain. One question kept going through his mind. "Did I make the right choice? " Despite what Auska had said he didn't feel confident about the choice he made at all. He had brought two of the most important people in his life back to this shattered city and all the pain and fighting. He knew the eva's weren't destroyed, he knew he would be needed to defend mankind again and it filled him with fear. Would he be able to defend people again, with the memory of his recent failure fresh in his mind?

As they rounded the corner the sight of Rei's shattered apartment building greeted them. There wasn't a single wall left standing. Rei was dumbstruck. The only home she had ever known was a pile of rubble. Rei allowed herself to cry. She sunk to her knees and sobbed. Auska was shocked, "(Maybe I was wrong about her being a doll. I should lay off her a little bit. After all she has been through all we have too.)" Auska knelt down next to Rei and tried to comfort her as best she could, "Rei it'll be okay. Come on you can come home with us, I'm sure Misato won't mind at all. Isn't that right Shinji?" It took Shinji a few moments to recover and reply. He was shocked. For as long as he had known Rei she had never shown a display of emotion as open as this. Not only that but Auska was actually trying to comfort her, "(I thought Auska hated Rei.) Of course it will be okay. Come on we're almost home." With that he knelt down on Rei's other side and attempted to comfort her, "Rei you are my sister and I will never abandon you. All three of us have lived through Third Impact and we share a unique bond. Auska and I will never abandon you, we will do everything we can to help you. Isn't that right Auska?" Auska looked wide-eyed at Shinji and then Rei before she nodded. "Thank you pilot Soryu." " Rei my name is Auska. We're friends so you can call me Auska, pilot Soryu is just too formal." Rei smiled at her new friend, "Very well, thank you Auska." Shinji was overjoyed, "(Maybe I made the right choice after all. They seem to be happy, now if I can keep it that way.) Come on girl's we're almost home." Shinji helped the two up and they continued the trek home.

X

In commander Fuyutski 's office, Misato was receiving a thorough debriefing from the commander. "As you know major someone has stopped third impact and spared us from SEELE. I believe that it was Shinji, as do you. The more important question is, where is he? The recovery teams reported that the entry plug was still inserted in unit 1 but Shinji was nowhere to be found. Likewise the plug was in unit 2 and Auska was also missing. We have had no luck finding them, doctor Akagi and Commander Ikari. However although we can't find them we believe them…" The comm. System in Fuyutski's desk beeped and he answered. "Ibuki here sir."  "Go ahead lieutenant."  " Very well sir. We still have had no luck in locating the pilots but we believe we have located doctor Akagi and commander Ikari. We believe they are in terminal Dogma and …"  "Very good lieutenant, continue looking for the children and I will deal with this situation, Fuyutski out." He shut off the comm. System, "major would you like to accompany me?" Misato smiled and pulled out her glock pistol,  "Wouldn't miss it for the world, its time for the commander to answer to me. And trust me I won't be gentle." Misato pulled back the slide and the distinctive sound of a round being loaded was heard. "After you commander."

X

The bridge was still in chaos as the staff attempted to come to terms with what happened in the last few hours. First there was the JSSDF, then SEELE and third Impact, the memory of Shinji in pain and finally waking up as if nothing had happened. The bridge bunnies were exhausted but they had to continue to work and attempt to turn the chaos into order. "Recovery team one concentrate on the recovery of unit 2 and place it in the repair cage. Team-2 recover unit 1 and place it in cage 1. All remaining teams concentrate on the SEELE Eva's and place them in subsequent cages. That is all."  Maya let out a sigh and pulled her headset off. "How long has it been now?" Aoba looked over at her and said, "It's been 36 hours straight, no breaks, no sleep and…" his stomach let out a growl, " no food."

"I hear that, what's happened to the relief team that was supposed to be here four hours ago?" Hyuga asked from his station. " I heard that they were drafted into one of the recovery teams for the Evangelion's. Apparently bridge staff welfare is a low priority for the new commander." Maya looked puzzled, " Is commander Ikari really dead? I mean just because we haven't heard from him doesn't mean he's dead." "I, for one, hope that he is long gone. He used us right from the beginning. He lied to us and expected us to follow him to hell and back without question. I hope he didn't make it back from third impact. It would do the world a favor if he didn't." Aoba's passion scared Maya so she kept quiet cut Hyuga started from the other side, "if he isn't dead he's gonna be hung out to dry. Now that everyone knows what he tried to do he will have no support either here or in the international community. My money is on Fuyutski to take over from him. If he isn't dead I bet Misato and Shinji would like to remedy that problem." Now Maya was worried,"(This is a mans life we're talking about. There's no denying that he has done terrible things but if we just kill him then we become just as bad as he is.)" With the worry still evident on her face Maya returned to giving orders to the recovery teams.

X

Deep in the bowels of the geofront two people stood in front of the massive doors to terminal dogma. "Its time major are you ready?" Misato's gun made its appearance, "As I'll ever be commander. Open the door." Fuyutski swiped his ID card through the reader on the door. The door opened slowly as the machinery fought to open the heavy door. The first thing that the officers noticed was that the red cross stood alone at the center of the LCL sea. Lilith has gone. Both officers moved slowly into the cavernous room slowly. Fuyutski constantly looking around trying to comprehend what happened, Misato was sweeping her gun from side to side, determined not to let Ikari get the drop on her. After advancing a few meters Misato stepped on the tattered remnants of a black jacket. "Commander I found something!" Fuyutski rushed to her side and inspected the bloody garment closely. " What happened here Gendo?" he muttered to himself. "He's gone, unit 1 had its revenge on him. He has lost his immortal soul and he will never return to this life." Both officers whirled around and Misato trained her gun on the intruder. "Ritsuko! Is it really you?" Misato was shocked at the sight of her friend. Her usually immaculate lab coat was tattered, torn and stained with LCL. The thing that scared Misato most was the haunted, empty look in Ritsuko's eyes. "He's gone Misato, Shinji had his revenge." Ritsuko knees buckled and she fell to the ground. Misato was there in an instant, cradling her friend's head in her lap, and trying to get her to wake up. Fuyutski pulled out his cell and dialed a number, "Medical Section this is commander Fuyutski. Dr. Akagi has collapsed in terminal Dogma. I need a medical team here immediately." He disconnected and stared grimly at the scene in front of him. "(Don't give up Ritsuko. We'll need you if we're going to beat SEELE.I have a gut feeling that we haven't seen the last of the 'old men'.)" He could do nothing but wait for the med team to arrive.

X

Finally the pilots had arrived at the Katsuragi apartment. Rei and Auska slept peacefully but despite his fatigue and no matter how hard he tried he couldn't follow them. He stood on the balcony and reflected on the day and his role in it. The one memory that repeated in his mind was Auska's death. He saw it over and over in his mind and wallowed in his own helplessness. "(Why could I not help her? I had the power and the ability but still I couldn't help. WHY? She means more to me than anything but I just stood by and let her die. What right do I have to be near her, I don't deserve to be in her presence.)" While absorbed in his thoughts Shinji never heard the door opening. The first indication that he wasn't alone was when Auska placed her hand on Shinji's shoulder. "Shinji why aren't you sleeping? You've got to be more tired than Rei or me but your still awake. Why?" Shinji turned to her and she gasped at the pain she saw in his eyes. "Auska, I don't deserve to be near you at all. I left you to die and didn't even try to help you. I'm pathetic. I don't deserve to be near you. You deserve far better than me. When Misato gets back I'm gonna leave. You'll be much better off…" "Shinji if you finish that thought I will throw you over that balcony, injured arm or not! Can you be a bigger baka than you are now! Who cares if you weren't there the first time? You did so much more than just save my life Shinji, you saved my soul. You saved the souls of everyone on this planet. You faced pain and suffering greater than anything in this world and you still managed to bring it back. You are a hero Shinji Ikari and I can think of no better person to have here with me than you."

Auska wrapped her arms around Shinji and put his head on her shoulder. "Auska thank you. I…" "Shh. Don't say anything Shinji. I understand. I saw your mind remember I know how you feel about me and guess what I feel the same. Now come on you have to get some sleep." Auska led Shinji away from the balcony and back inside as they passed Shinji's room he asked, "Auska my room is back there, where are we going?" "Rei's sleeping in your room stupid and I'm not gonna let my savior sleep on the couch. You're going to sleep in my bed with me." "With … you (oh man!). Wait don't you think we should talk about this? I…I…I mean we're so young … don't you think we should talk …" Auska cut him off with a glare, "Don't be a baka. This is sleep, that's all. If you get any funny ideas then I'm gonna hurt you so badly that you'll never be able to sleep with a woman in the future, got it Third Child?" Shinji quickly swallowed and nodded meekly. "Good now lets go." Shinji spent the night in Auska's arms as they brought some peace and comfort to each other as well as a refuge from the memories of Third Impact.

X

The night passed and the morning sun began to creep over the city as a new day dawned. Most of the Evangelion units had been recovered and the repair work had already begun on units 1 and 2. In the Katsuragi house three teens had woken up to the new day. Shinji was the first to wake up and he spent a few minutes just watching Auska sleep. "(My God she's beautiful)." As he watched her she slowly opened the eye that wasn't covered by the bandages and smiled at him. "Guten Morgen, Shinji." "Good Morning, Auska. Would you like some breakfast?" "Would you mind Shinji, I'm really hungry." Shinji slipped out of the bed and made for the door, "Sure, just give me a few minutes." As Auska watched him leave she thought to herself, "(Why didn't I see his worth before? How can he still stand to be around me after all I've done to him? I treated him like he was lower than dirt and still he wants to be around me. He even thinks he's not good enough for me. I'm really lucky to have met someone like him.)" Shinji's voice snapped Auska out of her thoughts and back to reality. She scrambled out of bed to go eat and found breakfast waiting on the table waiting for her. "Hey Auska. Help yourself. I 'm gonna go wake up Rei." As Shinji headed towards his room Auska could hear him calling out Rei's name. "(No it's I'm the one who doesn't deserve you Shinji Ikari, not the other way around.)"

As Shinji came back with a sleepy looking Rei in tow, Auska called out "Morning Rei. Did you sleep well?" "My rest was satisfactory Auska" was Rei's reply. "Man we have to work on your social skills Rei. You have to stop talking so formally when you amongst friends and family. Okay?" "I will attempt to Auska." Auska noticed that Shinji was on the phone and she wondered who he could be talking to. All the phone lines were down, weren't they? "Alright Misato, it's good to hear you too just don't shout into the phone alright…. Yeah we're all right but could you send someone to pick us up, I want to get Auska's injuries seen to… No, no, no nothing serious…Yeah Rei is here too…Just send someone to pick us up and I'll explain everything…Yeah that's fine…See you soon."

As Shinji walked back into the kitchen Auska bombarded him with questions, "Who was that Shinji?" "Misato, she's sending a section two car to pick us up in thirty minutes so you guys better hurry if you want to be ready in time." Shinji was ecstatic, Misato was all right. Inside he knew she must be but it was always good to get confirmation on his gut feelings.

X  

Misato was crying when she put down the phone. "(They're all right. Thank god they're all right.)" Her work wasn't done yet though, she still had a few calls to make, "Section two this is major Katsuragi I need you to send a car to my apartment to pick up the pilots…Yes all three are there…I don't care what's going on down there, I want that car heading to my apartment in the next five minutes or you are going to be out of a job, got it bub…Yeah well its too late for apologies now just do your job, understand…good." She still wasn't finished as she dialed another number, "Commander, major Katsuragi here. Tell Hyuga to call off the search for the pilots they have been located…My apartment sir…Yes I already sent a section 2 car to pick them up…Understood sir, I'll get conference room one ready for their arrival…And sir could you please have a doctor present, Shinji mentioned that Auska has injuries…No sir he didn't say…very well sir." As Misato left her office one thought went through her head, "(I need a beer)."

X

An hour later the children and senior Nerv officers had gathered in conference room one for the debriefing including a newly recovered Ritsuko, apparently she was only suffering from fatigue. Commander Fuyutski was chairing the debriefing. "Now we have all heard the pilots accounts of Third Impact and the match with what little we know at this time. People I believe that we have been given this second chance for a reason. There have been no reports of activity from SEELE since we have returned from Third Impact. My theory is that the council has gone underground in an attempt to avoid being captured. Every government in the world now knows what SEELE is and is making preparations to launch a huge manhunt for them." The commander paused and looked around at the gathered personnel. "However just because that SEELE has been forced underground does not mean that their threat has vanished. They are one of only two organizations on this planet that has the knowledge and technical resources to produce evangelion units. The other is of course us. The UN has reestablished our legal protection and we are to be the first and only line of defense against any further aggression on behalf of SEELE. To this end we are receiving increased funding to rebuild the city, regenerate the damaged unit 2 and construct four new evangelion units." A hand was raised among the staff, "Yes major Katsuragi." "Sir isn't four new Evangelions a bit of an overkill?" The Commander pressed a button on the screen behind him and a picture of the SEELE mass-produced Evangelion appeared on the screen. "This is the SEELE Eva. It has been dubbed the omega series by the science directorate. The unit is equipped with an S2 organ that gives the unit an inexhaustible supply of power. In addition to this the primary armament of the Eva is a duplicate of the Lance of Longinus and a progressive knife." The footage of unit 2 being skewered by the lance was played on the screen and Auska flinched. Shinji noticed this movement and put his arm over her shoulder to comfort her, meanwhile Fuyutski continues. " In addition the unit is capable of being armed with any of the weapon systems available to our Eva's. This means that these things are brutal killing machines."

"However we believe that SEELE has lost access to the dummy plug system so the will be forced to rely on human pilots. This is where we have the edge, we have the three most experienced pilots in the world on our side." Motioning towards the three pilots as he spoke. "By the time they manage to build up a sizeable enough force we will also have our six evangelions ready to go. We will not let SEELE get a shot at starting Fourth Impact. Dismissed." As people began to file out of the room the commander motioned for Shinji to stay. After a few minutes and some quick words to Auska, Shinji and the commander were alone. "Shinji I know I can never understand what you have gone through but I really need you to stay and help us. You are the best pilot that we have and unit 1 is the most powerful evangelion that we have, not to mention the only one that we have operational at this time. Please Shinji, will you help us?" In his mind Shinji relived the terrible memories of evangelion. But he also remembered what happened the last time he refused to pilot unit 1. Auska paid the ultimate price for his failure and he had promised himself that he would never let that happen ever again. "I'm not going to run from my destiny anymore commander. I will pilot unit 1. You don't have to worry about me running off again. I've found something worth protecting in this world and I will fight my hardest knowing I have to protect it." "Thank you Shinji. You have given so much to us and we have no way to repay you for it. Thank you Captain Ikari." Shinji spluttered, "C…Captain?" "Of course, if you are going to lead the evangelion team you are going to have some sort of formal rank within Nerv. I think a captaincy suits you." Shinji seemed to think it over for a second, "Well, thank you sir. I guess." 

X

Meanwhile in the infirmary Auska was having her injuries checked. As the doctor removed her bandages she was quite amazed. "Well Ms. Soryu, you appear to have no physical injuries what-so-ever. You are in perfect health. You are free to go." "Well about time, " Auska grumbled, "(Now where is that baka Shinji? He better not have left without me or he will be so sorry.)" The now bandage-less Auska stalked out of the room and nearly tripped over Shinji who was sitting just outside the door. "Watch where you decide to sit baka or next time you'll be sorry" Shinji stood up massaging his arm that Auska stepped on, "Sorry Auska I just wanted to know if you were all right." "Well the doctor gave me a clean bill of health and I'm okay to go. So where's Misato?" Shinji jerked a thumb over his shoulder, "She went with Rei to get some food 'cause she thought you might be hungry." Auska began to walk down the hall Shinji pointed to, "So what did the commander want?" Shinji slightly hesitated before answering, "H…He wanted to know if I would continue to pilot Eva. When I said I would he made me a captain." Auska stopped dead in her tracks, " He made you a what? Why you and not me? After all I'm the one who died. I've been piloting longer than you too. Man there's no justice in the world I tell ya." Meanwhile Shinji was desperately trying to calm the volatile Auska down. "Hey relax Shinji, I'm kidding. I couldn't think of any more deserving person than you." "Do you mean it Auska?" Auska glared at him furiously, "Of course I mean it you dolt! But if you ever try to give me an order I'll make sure you regret it, understand?" Shinji nodded quickly and Auska seemed to calm down. "Good now lets find Misato and get the hell out of here cause I'm starving."

X

Back at the Katsuragi household another delicious dinner complements of Shinji had just been consumed and the topic had strayed to last night. " So Rei I heard that you spent last night here where did you sleep?" "I slept in Shinji's bed. I do not know where my brother slept." Misato went to take another can of beer from the fridge when she stopped. "Hold it! Did you say brother? How is that possible?" Shinji decided to step in knowing the subject would be hard on Rei. "Misato, my father made Rei using my mother's DNA. Therefore she's the closest thing to a sister I have. Which makes me her brother. Understand?" Misato seemed to think for a moment before answering. "Actually it doesn't but the world stopped making sense to me a long time ago so I'll just accept it. But if she took your bed where did you sleep, Shinji?" Auska chose that point to enter the conversation. "Actually Shinji slept in my bed with me…" Misato exploded, "What? What the hell do you think you were doing Auska? I know you like to practice kissing with him but having…" "Misato!" Auska and Shinji yelled together. "Misato," Shinji continued in a lower tone of voice, "There was nothing like that going on between us. I love Auska, Misato, and after nearly losing her during Third Impact I never want to lose her again. I couldn't sleep because I was haunted by my failure to protect her. But when I held her all the bad memories left me and I found peace. I love her and I never want to lose her again but we will not rush into something like that. I'm happy to take our relationship slow and she is too. But I think that we have done enough for this world to earn some trust and to not have people jump to conclusions about us. Please Misato I don't ask for much so please give me this small happiness?" Misato looked long and hard at the two and thought hard about it, "(Maybe they're right. They do deserve a little trust from me. They finally found something worth fighting for in this world and it's each other. I can't take it away from them. All right I'll give them a chance but if they mess up…) All right you can continue sleeping together provided nothing 'unseemly' happens, understand?" As both teens nodded she continues, "I'm going way out on a limb here guys so don't make me regret it. Rei, if you want you can continue to use Shinji's room and live here with us our you can find another place to go, it's up to you." Rei nodded solemnly before answering, "Thank you, I will remain here with my brother."

Misato nodded. "Well that's good to hear. It's time to get some sleep because we've got a busy couple of weeks ahead of us."

To be Continued… 

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Well that's the first chapter of Neon Genesis Evangelion: The Fourth Apocalypse. Any compliments, suggestions or criticisms, please send them to garygregan@eircom.net. Please don't flame me too much.


	2. Tokyo3's Reconstruction

Neon Genesis Evangelion: The Fourth Apocalypse 

Disclaimer: I don't own Evangelion, its characters, technology or anything else related to the show, so please don't sue me 'cause I don't have anything worth taking.

Notes: This is the second chapter of my first fanfic and I'd just like to thank the people who reviewed the first chapter. Thanks a bunch. Character thoughts are still in brackets.

Chapter 2: Tokyo-3's Reconstruction.

At the Katsuragi household Misato was still trying to get used to the new arrangements in the apartment. Although she had given permission for Auska and Shinji to sleep in the same bed, she still felt a little uneasy. She trusted Shinji implicitly, he gave her his word nothing would happen and she trusted him. It was Auska she was worried about. If anything was going to happen she would be the one to start it. Rei seemed to be adjusting well to her new living arrangements in the apartment and had proved herself to be a good cook, just like her brother. This was a real blessing because Shinji couldn't cook all the time and having Rei cook was a better prospect than eating Misato's cooking. Shinji had changed too since Third Impact. He had a new since of confidence around him. She thought it had something to do with Auska. After all she wasn't insulting him every five minutes like she used to anymore. "(If some one told me three weeks ago that those two would be together I would have recommended that they see a shrink. Despite everything that's happened I'm glad that they found happiness with each other, nobody deserves it more.)" Rei was cooking breakfast behind her and seemed to be happy, she was even smiling. "(That's another big change. I've never seen her smile before. Gendo must have done some horrible things to her to strip her of all her emotions like that. Shinji and Auska have been trying hard to get her to show more emotions and they seem to be succeeding.)"

Shinji and Auska stumbled into the kitchen and sat at the table. Auska's hair was tousled and Shinji didn't look that good either. Misato immediately jumped to one conclusion but she dismissed it just as quickly. "(They gave my their word and I trust them. I have to stop thinking 'that' whenever I see them come out of their room.) Morning guys, sleep well?"

"Well enough Misato." Replied Shinji before digging into the breakfast Rei placed in front of him. Misato nodded and continued, "Good to hear. Don't forget you guys have a sync test scheduled for today." Auska decided to make her presence heard. "Why do we have to go for a test anyway? Unit 1 is the only Eva that's online. So why do we all have to go in? Shinji should be the only one who has to go, not us too!" Misato let out a sigh, "Commander Fuyutski wants to make sure that you don't get rusty as the repairs to unit 2 and unit 0's reconstruction will not be complete for another month and the new Eva's another two weeks after that. If you wait too long your sync ratio's will drop through the floor and as operations commander I can't let that happen can I?" She looked around almost daring Auska to contradict her. Auska seemed to get ready for a major argument with Misato but Shinji cut her off before it began, "Okay Misato we'll be ready."

X

The reconstruction of Tokyo-3 moved at a rapid pace since the UN had allocated new funding for the city. Shinji looked out at the city that was slowly rising from the ashes. Unfortunately Misato's driving had not improved since the last time Shinji was in the car. After nearly hitting four mobile cranes, six dump trucks and twenty individual workers, Misato had finally slowed down and was proceeding at was a normal person would consider a safe pace. Most of the city outskirts had been restored and people had begun to return to the city. While this was obviously a good thing, it had a down side too. Three days ago Shinji, Auska and Rei had received notices that enough students had returned to Tokyo-3 so school was restarting next week. While Shinji was looking forward to seeing his friends again but he was afraid that his new status of 'Mankind's Savior' would attract a lot of unwanted attention from his other fellow classmates. Auska noticed Shinji's downcast mood and decided to leave him be. He had been spending a lot of time in thought since Third Impact and she decided it was best to let him think. She just hoped that if he had a problem that he couldn't deal with on his own, that he would come to her for help. 

X

The sync test was about to start. The pilots were sealed into their test plugs and were ready to begin. "Alright guys you've done this hundreds of times before. Just think of it as another sync test." Ritsuko was giving the pilots their pre-test talk while Maya prepared to start the test. Ritsuko nodded to Maya and Maya opened a comm. link to the children, "Beginning test now." As the test begun Maya carefully monitored the readings from the pilots. After five minutes she let out a gasp that drew the attention of Misato and Ritsuko. "What's wrong Maya?" Maya double-checked the readings before answering, "These readings are just unbelievable. Shinji's sync ratio is holding steady at 96.85%. Rei and Auska are holding at 90.8%." Both Misato and Ritsuko looked shocked. "That's impossible. How can they have had an increase of that magnitude in such a short time? It's just inconceivable." Misato seemed lost in thought while Maya and Ritsuko were trying to come up with an explanation for this. "(Is it because they have become closer together since Third Impact. Or is it something else? The commander was right about us having an edge in those kids. They will be the ones to shape the future of the human race not SEELE.) Don't look a gift horse in the mouth Ritsuko. Who cares how they managed to do it as long as they have, right? After all how much do we really know about the interaction of the evangelions and their pilots? Lets just leave it go, alright?" Ritsuko took one last look at the monitor showing the three pilots and shrugged. "Guess your right Misato."

X

The rest of the week passed too fast for Shinji's taste and all too soon it was Monday morning. The day of his return to school. He was dreading it and looking forward to it at the same time. Auska on the other hand was complaining very loudly to anyone in earshot. "Why do we have to go to school anyway? We did save the world after all and I've already been to college. So I should at least be able to stay home." Misato always repeated the same reason, Auska was to young to not be in school and that was that. Rei seemed, as usual, indifferent to it all but Shinji felt that he could feel a sense of anticipation from her. Finally after all the arguments and yelling they were walking to school just like they used to in the 'old days'. The school had been the first building to be repaired and the heavy machinery could still be seen scattered about the city. Shinji had heard from Misato that the city would be fully reconstructed in three weeks, the same time that unit's 0 and 2 were scheduled to be reactivated.

As they neared the school Shinji felt his sense of dread growing, "(How much will they remember about it? Will they blame me for destroying paradise? Will Kensuke and Toji be there? Will we still have the same boring teacher?)" Shinji was so wrapped up in his thoughts that he didn't realize they had reached the school. It was just like he remembered it. At his approach the students chatting outside fell silent and stared at him and the girls. Before Shinji could even mutter a greeting he was surrounded by swarms of students bombarding him with questions, "What was it like?…Were you scared?…What did it feel like to be a god?…What did you do to stop it?" Shinji felt himself overwhelmed with anger. Didn't these people know what he'd gone through? What he had experienced? What he had to sacrifice? Auska could see Shinji begin to lose control but couldn't do a single thing to stop it. She was surrounded by her own group of 'fans' and couldn't move an inch. Just as Shinji felt as if he were about to explode he heard a familiar voice from the crowd. "Get away from him you vultures. Anyone who's not gone in the next five seconds will feel my fists, understand? 1…2…3…4…" Before he had even reached five the crowd had scattered. From where he had slumped to the ground Shinji looked up and saw his rescuer. Toji Suzahara was standing in front of him flanked on either side by Kensuke Aida and Hikari Horaki. "Hey Shinji, long time no see." Shinji was speechless, Toji looked uninjured. He wasn't missing a leg. He was whole. "Toji what happened to your leg?" was all Shinji could manage to say. "Well to tell you the truth I don't know. When I returned from Third Impact it was just whole again. The doctors were stumped too. They ran loads of tests but since they couldn't find anything wrong they let me go. By the way Shinji thanks for saving our butts. I know it must have been hard and I know thanks doesn't cut it but it's all I got." He extended a hand to help Shinji up and Shinji took it. "Its okay Toji. Just seeing you guys safe is reward enough. Come on or we'll be late for class."

The rest of the day passed pretty uneventfully. Well uneventfully by Shinji's standards. After this mornings near assault Auska became very protective of Shinji. She almost killed anyone that came near Shinji with the intention of asking a question. Finally Kensuke asked Shinji what was up, "Don't deny it Shinji. She has been acting awfully protective of you lately, so come on spill it." " I don't know how to explain it Kensuke. Its just like we've connected on a deep level. She is everything that I've ever wanted in my life. And I'm terrified that I might lose her some day." Toji looked over with an 'are you an idiot look' on his face, "Shinji, I know that I'm not the brightest when it comes to women but from the way she has been acting today that she deeply cares about you too. She has made sure that not one person with a question has come within fifty feet of you since this morning. Your lucky to have found that kind of companionship Shinji." "(Maybe Toji's right, maybe I don't have anything to worry about after all.)"

On the other side of the room Auska had just finished chasing away the last would be questioner and was talking with Hikari. "Alright Auska, what's going on with you and Shinji? You have been protecting him all day from those vultures. You can't be doing it out of the kindness of your heart. So what's up?" Auska seemed to think for a moment before answering, "The truth is that when I'm with Shinji nothing else matters. He is the one I have been waiting for all my life. He's kind, considerate, and a good person. He even thinks that he's not good enough for me. Hikari, he did much more than save my life. He saved my soul. He made me see my own self worth. I…love him Hikari. But I'm terrified that he's going to find someone better to share his life with." Auska looked over at Shinji who seemed to be in deep conversation with the stooges. Hikari looked at the expression on her face and sighed. "Auska you're the smartest person I know but sometimes you can be a real idiot. I've known you two should be together since the day I met you and by the look on your faces when you see each other both of you have realized it too. He will never leave you Auska just like you will never leave him." "(Maybe Hikari's right, maybe I don't have anything to worry about after all.)" 

X

The weeks passed in Tokyo-3 and the reconstruction of the city had finally ended. Deep in the geo front a different kind of reconstruction had also ended. In his office commander Fuyutski was looking over the information on the completed Eva models. Unit two had been repaired and the four new Evangelions had been constructed. With the massive injection of funds and personnel from the UN the new Eva's had been swiftly completed. Now all he had to do was find new pilots for them. After scouring the personnel databanks he came upon the perfect choices, one even had previous Eva experiences. "(Shinji will hate me for this but I have no other choice. Please forgive me Shinji.)" He dialed a number on his cell. "Major Katsuragi we have something important to discuss. Meet me in my office at ten am tomorrow morning, and bring Captain Ikari as this concerns him too."

X

The following morning Auska and Rei were left in the apartment alone, as Shinji had been called away for some meeting with the commander. "This sucks!" Auska was complaining to nobody in particular, "It's a Saturday and I can't even go out with Shinji because he has been called away for some meeting with the commander. I'm stuck here with Rei…" Auska suddenly stopped in mid sentence as an idea struck her. "(I bet Rei has never been shopping before. Shinji did say we were to help her become more normal and after all what's more normal than shopping. Maybe I can get Hikari to come along too.) Rei." The blue haired girl looked up from the book she was reading, "Yes Auska." "Have you ever been shopping before?" "I have heard of the practice but have never engaged in it before. Why do you ask?" 

"Well because I think that it's time to introduce you to the fine art of shopping. Besides you could use some new clothes anyway." Rei thought for a moment, "Very well I will accompany you on this shopping trip," "Great just let me call Hikari and leave Shinji and Misato a note and we'll be off. (This is gonna be great.)"

X

"Good to see you again Shinji, I hope you are well." "As well as can be expected commander." The commander motioned for Shinji to sit and Shinji complied. "Let me get straight to the point Shinji. The new Evangelions have been completed and suitable have been located. The pilot's names are Toji Suzahara, Kensuke Aida and Hikari Horaki. These candidates are …" Shinji just exploded. "What do you think you are doing! Do you choose my friends by accident or do it deliberately just to torment me! You remember what happened the first time Toji was inside an Eva, don't you? He almost lost his life. How can I ask him to get into an Eva again? How do you expect me to ask them to risk their lives?" 

"I can ask Shinji because we have no choice. Suzahara has already had some limited pilot training and Since Aida and Horaki are friends of you and Auska they will be more receptive to you and easier to train. Please Shinji I wouldn't ask if the situation wasn't dire. Recently the UN has been monitoring a number of large cash transfers from rogue nations and criminal organizations to some unknown organization. I believe it to be SEELE. The amount of money involved here is enormous Shinji. Enough for SEELE to construct a number of their Omega class Eva's. We need pilots badly Shinji and these three are the only ones who can be ready in time. Shinji I know I have no right to ask this but if SEELE gets their way all life will be wiped out and you friends will die anyway. At least this way they will have a chance to change that."

Shinji seemed to calm himself, but not by much, "If anything happens to them then you will pay Fuyutski. When will they be told?" Fuyutski let out a sigh of relief, "Tomorrow, with the first sync test scheduled for the day after." Shinji continued to glare at the man, "Alright Commander, but remember my warning."

X

In the Tokyo-3 mall Auska was in her element. It had been so long since she shopped that she almost exploded when she saw the new mall. So far she had dragged Rei and Hikari to half the clothes shops in the mall. So far Rei had picked up a new sundress, five new blouses, four pairs of pants, a jacket, three skirts, a dozen new T-shirts and five sweatshirts, all in shades of blue. Hikari was content to watch Auska teach Rei how to shop and soon the three girls had collected a mountain of shopping bags. This blistering pace continued until they reached a formal clothes store. All three just stood there admiring the dresses until Auska made a move, "Well don't just stand there lets go inside and take a look." Auska led the way and began to search for her ideal dress. "Well guess we better join her." Rei simply nodded her head and followed. After a while they had found their ideal dresses. Auska stepped out of the changing room in a full-length dress. The dress had a bare back and was cut in a way to show off a lot of cleavage. The dress was just a shade darker than her hair and contrasted well with her eyes. Next came Rei. Her dress was done in a wispy light blue and flowed more than Auska's. It was also more conservatively cut than Auska's not showing off as much but was still stunning nonetheless. Hikari's dress was pure white and seemed to shine under the stores lights. It was more conservative than Rei's but it suited Hikari perfectly.

"Since we all look so good I think we should buy these dresses, don't you guys think so?" Auska performed a small twirl to emphasize her point. Hikari took one look at the price tag and almost fainted. "I can't afford this. It would take me six months to earn enough for a deposit." "Don't worry Hikari. We'll buy it for you." Rei surprised both girls with that offer and they stared dumbstruck at her. "Did I say something wrong?" Hikari continued to stare but managed to respond, "I can't accept a gift like that. It's just too expensive." Auska shook her head firmly, "Don't worry about it. Shinji makes captains money now so we don't have to worry. Hurry up and change so we can pay for these dresses." Less than ten minutes later the three girls left the store carrying their dresses and the mountain of other shopping bags that Auska and Rei had accumulated over the course of their day. "(I am really lucky to have friends like this.)" Hikari smiled to herself as she looked down at the box containing her dress. "(Wait until Toji sees me in this.)"

X

Auska and Rei finally made it home to find Shinji standing on the balcony again. Both girls decided to leave him alone as the put their purchases in their respective rooms. This was a colossal task and took them a good fifteen minutes. Even after that time Shinji still hadn't moved from his spot on the balcony. "That's it I'm going to talk to him!" Rei looked concerned, "Do you think that is wise, maybe he wishes to be left alone." "I don't care. He has to realize that we are here to help him with his problems now and by the looks of it he has one big problem on his hands." With that she picked up a jacket and moved to the balcony. "(How can Fuyutski do this? Is he trying to hurt me on purpose or is this his sick idea of a joke? Just remember Fuyutski I meant what I said. If any harm comes to them you will pay.)"

Even when she was standing right next to him he didn't notice her until she draped the jacket she was carrying over his shoulders. Shinji jumped and looked at her accusingly and was surprised at the anger he saw in her eyes. "What do you think you are doing? I was willing to overlook this at the start but now its getting annoying. You spend more time thinking about your problems than anything else. Listen to be Shinji, I admire your strength and your intensity but you can't deal with every problem on your own. Rei and I are here to help you. Tell me what's wrong." Shinji was amazed at how fast she could change from being angry to being sympathetic and helpful, "(She is so beautiful. Maybe I should take her advice.) The commander has chosen the new pilots for the new Eva's." "Anybody we know?" Shinji nodded sadly, " It's Toji, Kensuke and Hikari." Auska was shocked. "Before you completely lose it let me explain what the commander said. Shinji relayed the conversation he had with the commander. "Although I hate to admit it, the commander's right Shinji. We need pilots and those three will be the fastest to train. I can see why you're angry Shinji but we have no choice. Now come inside where it's warm." Shinji smiled at her, "I'll just be another few minutes." "Well don't be long." As Auska brushed past him she kissed him on the cheek. Shinji merely stood there with his hand to his face. "(I so do not deserve her.)"

X 

As Monday came Shinji wondered if Toji, Kensuke and Hikari would agree to fight. They were scheduled for their first group sync test in less than four hours. After that they would try to activate their new Evangelions. Breakfast had already been consumed and the children were just lounging around waiting to leave for headquarters. Misato had to go in early to get things ready for their arrival, including getting new ID cards ready for the new pilots, if they show up. That left Shinji, Rei and Auska to walk to Nerv HQ where the others would be waiting. Finally Shinji decided it was time to leave so all three left. Nobody said a word on the walk. Shinji and Auska were worried about their friends and the danger they would now face. Although she didn't show it Rei was also worried. She has seen what Eva had done to pilots over the years and did not want anyone to be hurt.

As they neared the entrance to the great underground bas a small knot of people came into view. It was the others. As Shinji got closer he could see the worry and nervousness on their faces. Everyone tried to act cheerful but nobody was fooled by the act. The six children descended into Nerv in silence. Shinji finally spoke up. "Hikari you go with Auska and Rei to the girls locker room. Toji, you and Kensuke follow me." With that the little group separated. In the locker rooms the more experienced pilots helped the new recruits into their plug suits. Toji remembered how to get into his but Kensuke was having a lot of trouble. 

After what seemed like an eternity all pilots assembled in the test chamber where Ritsuko was waiting for them. "Good morning. I am Dr. Ritsuko Akagi and I will be in charge of the tests we will be performing today. This test is to measure your compatibility with an Evangelion. The more experienced pilots will be going first to demonstrate how it is done. After them it will be you turn. Toji plug suit was black, much like his old one. He seemed to be the most worried. Not surprising considering the last time he was in an Eva he almost died. Kensuke, in a military green plug suit, on the other hand was excited. His dream was finally about to come true. Hikari was the most openly afraid one but was determined to do her best for her friends.

As the new pilots watched the test began. Technicians began to take readings and measurements from the pilots as they sat in the test plugs. "They seem to have gone up a few points since last time" "How much?" Maya checked the readings again. "Shinji is at 98.2%, Rei is at 94.4% and Auska is at 95%. All in all they're doing well." Ritsuko seemed satisfied. "Okay get them out of there and prep the new pilots." In less than five minutes the situation had been reversed. Auska, Rei and Shinji were now watching Toji, Kensuke and Hikari.

"Begin the test." Hikari was the most freaked out by the LCL but she was trying to be strong. Toji was concentrating with his eyes closed and Kensuke was trying to inspect everything in the plug. "Maya results?" Maya checked her readings. "Pilot Suzahara is at 34%, not bad considering the length of time that he has been away from an Eva. Pilots Aida and Horaki are at 21%." Ritsuko was impressed. "Not as good as Shinji's first attempt but not bad none the less. Get them out of the plugs and we'll prepare for the activation tests."

X

In the standby room the new pilots were exhausted. Throughout the day the tests had continued and the Eva's had been successfully activated. On seeing his new green Eva Kensuke almost had a heart attack. Hikari and Toji were a little more dignified. Toji's new unit 3 looked the same as his old unit, which caused him to shudder when he first saw it. Hikari's unit 5 was white with a red trim. When she first saw it she just stared at it in awe. It was one of the machines that would protect this world and she was to be its pilot. Auska and Rei were there too but they weren't as exhausted as the others. "(Must be used to it.)" Hikari thought to herself.

Meanwhile Shinji was being briefed on the capabilities of the Eva's under his command. "As you know Shinji we have been researching ways to incorporate SEELE Eva technology into our units. We have succeeded in integrating S2 organs from the SEELE Eva's destroyed during third impact into our own units. The Eva's will no longer have to rely on an umbilical cable to supply their power. In addition we have enhanced the capabilities of the progressive knife. Using the new supply of power we have been able to double the knifes cutting power making it an unequaled weapon in close combat. In addition we have developed upgrades for the standard pallet rifle. Once again using the S2 organ we can channel a stream of high-energy plasma into the weapon and are capable of discharging it all at once. The resultant beam is three times as powerful as a positron rifle but has two major drawbacks. Its long charging time and the fact it can only be used once before the rifle explodes. All other aspects of the Eva's remain the same as the previous units. Dismissed Captain." Fuyutski finished his briefing and left the room. "(Its as if he thinks that we're going to be attacked at any time. Unfortunately it's going to take some time to get the others trained well enough for combat.)"

Shinji entered the standby room and took in the atmosphere of gloom that pervaded the room. "(Got to do something about this.) Come on guys cheer up its not the end of the world. Lets go get some dinner, on me." Everyone seemed to perk up at the mention of dinner, especially Toji. "Its on you right? And we can order whatever we want?" Shinji nodded, "Well then, what are we waiting for?" Toji rubbed his hands with glee. As Auska led Shinji from the room he thought, "(What have I gotten myself into.)"

**To Be Continued…**

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Well that's the second chapter. The training will continue in the next chapter and maybe some romance will sparkle too. For those of you waiting for some action, fear not it will be here soon. Any suggestions are always welcome.


End file.
